University Of Rochester

NSF Awards · FY 2024 · 2024-06

Mobile devices, such as smartphones and tablets, embed multiple processors to efficiently carry different types of computation. In such systems, applications running on different processors store their data on a single shared memory. This project uncovers certain security vulnerabilities that mobile systems with shared memories possess. Leveraging these vulnerabilities, a malicious party could circumvent existing protection mechanisms and extract sensitive information by monitoring data access patterns. The research will develop a framework to better understand potential attacks and investigate several protection mechanisms. Broader comprehension and mitigation of these attacks hold crucial importance in protecting intellectual property and user privacy in mobile devices. The award contributes to enabling a more secure operation of billions of mobile devices used daily around the globe. This project investigates a critical side-channel leakage mechanism based on the memory-access contention occurring when multiple applications execute together in a multi-processor system with shared memory. An adversary could exploit this leakage to build attacks and extract intellectual property, such as the hyper-parameters of neural networks used in biometric authentication, without requiring special privileges or comprised hardware. This project builds upon an attacker framework to extract unique memory-contention-based signatures of victim applications. New profiling and analysis techniques are developed to capture non-linear memory access characteristics of machine learning and artificial intelligence workloads. The signatures are then used to create reverse-engineering, information extraction and denial-of-service based attacks. Finally, various countermeasures at architecture- and system-level are developed against the new attacks. The research team investigates the security, performance, area, and energy implications of new memory controller scheduling policies and randomization-based solutions. This project unveils a previously overlooked class of cybersecurity threats with financial and privacy-related impacts. The awareness and mitigation of the new security issues strengthen the trustworthy operation of billions of mobile devices. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NSF Awards · FY 2024 · 2024-06

This CAREER proposal uses seismology and machine learning to explore questions about the structure and formation of the Earth's crust beneath the ocean. The processes that form and shape the chemical and physical properties of the rocks beneath the seafloor are different from those associated with the rapid and voluminous volcanism generated during the creation of large undersea volcanoes and ocean-islands. While many aspects of these processes are well understood, questions remain about the details and causes of the boundary between the stiff rocks (lithosphere) and the weak interior (asthenosphere). It is still unclear how the uplift and emergence of large oceanic plateaus and ocean islands is related to deep volcanism or shallow thermal cracking. These questions will be investigated by using machine learning to image the subsurface of the largest ocean-basin using existing seismic data. Pacific-wide imaging using ground vibrations is expensive and challenging. The seafloor is sparsely instrumented and the data noisy. Artificially intelligent algorithms will be trained to extract useful information from noisy seismic data, and the signals will be used to reconstruct 3D wave speed images of ocean interior. The improved resolution of the ocean subsurface informs tests of models explaining ocean plate genesis and evolution. Students will be recruited and trained using project-based courses that prepare them for research careers in academia and industry using state-of-the-art tools and resources. The educational plan includes two new project-based courses: “Seismic Signals & Noise” and “Earth Imaging and Machine Learning,” which closely integrate with the research questions and provide learning and research experience for undergraduate and graduate students. Multi-scale deep probabilistic seismic imaging is the process of reconstructing ‘uncertainty-aware’ images of a planet’s interior by stitching together wave signals extracted from sparse and noisy ground-vibration data (earthquake and ambient noise body-waves and surface waves) using sensor arrays with different space-time footprints (small and large aperture as well as short and long duration deployments). This approach uses artificially intelligent machine learning algorithms to solve data and model prediction steps in the image reconstruction problem. Step 1, cleaner signals: improved wave detection by denoising the long-period (SS, PP) and short-period teleseismic body-wavefield (Ps- and Sp-RFs). Step 2, improved images: joint modeling of the waves through a realistic and adjustable 3-D mesh takes advantage of waves propagating with different sensitivities. Step 3, fast reconstruction with errors: a probabilistic inverse modeling generates a large ensemble of models from which uncertainties can be estimated. This framework requires that many images are generated in step 2 and the process iterated. Again, intelligent algorithms, such as generative AI, are used to speed up, learn, and compress the model ensemble. The software and algorithms developed will contribute to the exploration of planetary interiors in situations where data is often sparse and noisy. This project is jointly funded by the Geophysics program and Education and Human Resources Program in the Division of Earth Sciences and the Marine Geology and Geophysics program in the Division of Ocean Sciences. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-06

Home-based exposures and poor housing quality contribute to health. problems including asthma, lead poisoning, reproductive disorders, etc.. Household exposure research can inform prevention and mitigation strategies. Responsible report-back of individual-level research results (RBRR) from household exposure studies is essential to inform behavioral, housing infrastructure, c, and solutions to improve health. While high level report-back principles have been developed for environmental health research, these do not provide specific guidance on the unique ethical challenges of household exposure research. RBRR for household exposure studies raises a number of ethically contentious issues related to the actionability of results, participants’ housing status (e.g., income level, owner/renter, public/private housing), and the interests of third parties (including family members, neighbors, health professionals, landlords and community leaders), among others. This project aims to develop guidelines for RBRR for household exposure studies in ways that respect participant preferences and communicate information appropriately. We build on a longstanding community partnership with Rochester Energy Efficiency and Weatherization (RENEW) and actively involve a Stakeholder Advisory Board that represents the perspectives of community groups, housing providers, IRBs, public health professionals and others who may be affected by RBRR. We integrate prior report-back studies by recruiting participants from several past housing exposure research studies, including the recently completed Rochester-based ROC HOME study, to provide formative input to Aim 2. Successful completion of this project will result in: (Aim 1) a philosophically and empirically-informed typology of the key ethical questions faced by researchers during RBRR of household exposure studies; (Aim 2) a tool for eliciting participants’ preferences for RBRR in household exposure research; and (Aim 3) decision-support guidelines to help research teams return individual results responsibly. Our collaborative approach will use a rigorous transdisciplinary framework to fill a crucial gap in report-back guidance for household exposure research and will serve as a model for future research on report-back of environmental and non-genomic research results.

NIH Research Projects · FY 2025 · 2024-06

PROJECT SUMMARY Older adults ≥75 years represent the fastest-growing population to initiate dialysis in the US. These people face challenges in decision-making around dialysis initiation. They have reported that clinicians seldom elicit treatment preferences, discuss prognoses, or explain the tradeoffs of kidney therapy (KT) options. Older patients often prioritize the quality of life over life prolongation. However, dialysis is still commonly presented as the sole KT option without any discussion of conservative kidney management or the effects of dialysis on the future quality of life. Subsequently, many of these patients experience deterioration in quality of life, experience high healthcare utilization rates, and undergo intensive end-of-life (EOL) treatments. Indeed, KT decision- making requires the engagement of patients and physicians alike—incorporation of patients' goals, discussion of alternatives to dialysis such as conservative kidney management (CKM), conversation about prognosis and exploration of patients' emotional needs. The proposed study is a type-1 hybrid effectiveness-implementation trial of a palliative care (CKD-EDU) intervention for patients ≥75 years old (n=326) with an estimated glomerular filtration rate (eGFR) of ≤ 30 ml/min/1.73 m2. Patients in the intervention group will receive 1) a multicomponent video and paper KT decision aid including a question prompt list, and 2) coaching from a palliative care clinician. The visits will be used to explore patients' goals, address KT information needs including prognosis, and attend to their emotions to aid them with KT and EOL decision-making. Patients in the Control Group will receive the usual care from their nephrologist and a dialysis educator. Aim 1: To determine whether CKD-EDU improves the kidney therapy decision-making process (primary) as measured by the Decisional Conflict Scale at month 1 and enhances patient well-being (secondary) as measured by the Burden of Kidney Disease Subscale at month 6. Aim 2 (secondary): To determine whether the intervention reduces six-month health services utilization and improves end-of-life care course during the last 30 days of life. Aim 3 (exploratory): Identify barriers and facilitators to the dissemination and implementation of CKD-EDU using rapid qualitative inquiry with key stakeholders (e.g., patients, caregivers, nephrologists and palliative care clinicians).

NIH Research Projects · FY 2025 · 2024-06

PROJECT SUMMARY/ABSTRACT Fetal alcohol spectrum disorders (FASD) are a highly prevalent neurodevelopmental disability yet extremely underserved by systems of care. FASD is linked to varying abilities in areas of executive function, attention, memory, adaptive skills, and emotion regulation. These emotion regulation difficulties are associated with 90% of individuals with FASD having co-occurring mental health disorders. However, no evidence-based mental health treatments have been adapted or tested for this population. This gap is particularly salient for the adolescent period, as many of these co- occurring disorders arise during this developmental timeframe. Dialectical behavior therapy for adolescents (DBT-A) is an evidence-based cognitive-behavioral therapy that specifically targets the biological predisposition for emotion dysregulation and invalidating environments that adolescents with FASD commonly experience. DBT-A is an intensive treatment program, involving weekly skills groups with adolescents and their caregivers, weekly individual therapy for adolescents, and 24/7 phone coaching. The proposed project aims to adapt DBT-A for adolescents with FASD and their caregivers and test the feasibility of the adaptations in a community mental health clinic. Given low FASD awareness among community clinicians, this project will also involve the development of trainings for mental health clinicians on FASD. Implementation science, specifically the EPIS framework (Exploration, Preparation, Implementation, Sustainment) and attention to social determinants of health will guide the conduct of the project. Input from a community advisory board consisting of adolescents with FASD, caregivers, and mental health clinicians will be prioritized at every step of the EPIS process. The aims of the proposed project are as follows: Aim 1- Systematically develop materials for FASD-informed DBT-A administration utilizing the EPIS implementation framework; Aim 2 - Conduct a feasibility trial of DBT-A with adolescents with FASD and their primary caregiver. The proposed project is an essential foundational step to address the gap in mental health care for individuals with FASD, as well as assist mental health clinicians in best serving this population. The feasibility of this project is supported by emerging research adapting DBT to other populations with neurodevelopmental difficulties. As this project will take place in an existing clinic in the community, it allows for careful examination of implementation factors that could support future generalizability to other existing mental health clinics. Additionally, the proposed project will provide mentored training to prepare the PI for a career as an independent researcher. Through the support and guidance of experts in the fields of FASD, intervention, implementation science, DBT, and social determinants of health, the PI will gain essential competencies in mental health intervention development, rigorous implementation and dissemination processes, and community-member engagement.

NSF Awards · FY 2024 · 2024-06

Both children and adults often display essentialist biases—assuming that groups, such as biological species, are uniform in their features—which can lead them to underestimate variability within-species and across generations. This project will examine learners’ understandings of biological variability, a key foundational concept in biology education, that is linked to understanding genetics and inheritance. The researchers will investigate the connection between children’s essentialist biases and their reasoning about the extent and dimensions of biological variability within species. The researchers will conduct a longitudinal study with four to twelve year old children and with adults to chart a clearer picture of how ideas about trait variability develop. This research will provide new insights into children’s categorization of species and into changes in children’s understanding of biological variability that occur with age and experience. This could ultimately allow educators to develop science education interventions targeted to individuals that are designed to increase students' understanding of this core biological concept and to allow understanding of biological variability and genetic inheritance to be evaluated more precisely. This project is supported by the ECR program which supports fundamental research that generates foundational knowledge that advances the research literatures in STEM learning and learning environments, broadening participation in STEM, and STEM workforce development. This proposal will investigate the development of learners' beliefs about biological variability in terms of phenotypic traits and their inheritance. Current methods in educational research for assessing students’ understanding of variability are typically cognitively demanding and time-consuming and have only been able to capture a coarse picture of children’s notions of biological variability. This proposal will introduce a cutting-edge method of mathematical modelling called Markov Chain Monte Carlo with People (MCMCp), an adaptive computer algorithm designed to assess and explore individuals' understanding of biological categories more accurately. MCMCp infers how representative or probable individual category members are in an individual’s category representation. It does this without having to specify all experimental stimuli a priori. Instead, the method explores children’s notions of representativeness adaptively– that is, it uses the learner’s previous responses in the task to inform which stimuli should be presented to the learner next. Using this approach will enable a more precise characterization of children’s and adults’ species concepts and the extent to which they accept variability in phenotypic expression within a species. The researchers will assess learner’s assumptions about within-species variability across a range of traits and organisms as well as their assumptions about genetic variability--variation between parents and offspring. They will also study non-animal categories (one natural kind, one artifact) to understand whether and how essentialist biases apply to non-biological kinds as well as biological kinds. This research will lay a foundation for designing effective, individualized early education curricula for central biological concepts. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

NIH Research Projects · FY 2026 · 2024-06

ABSTRACT Deaf and hard of hearing (DHH) children often have limited or delayed access to language during early childhood, which has harmful consequences for language acquisition and many aspects of child development. While there have been great strides in technology and available interventions to support language acquisition, there is still tremendous variability in language skills and development outcomes of DHH children. This is in part because families have to navigate a complex landscape of early interventions while deciding how best to support their DHH child. The first aim of this project is to document how families plan and manage language learning for their children using a series of interviews and surveys. A major challenge in understanding how best to support DHH children is that without centralized ways to find families, most research studies recruit participants through organizations like cochlear implant clinics and school programs, and focus on just a subset of DHH children (e.g., just those learning ASL, or just those using cochlear implants). This raises issues of sampling bias – children affiliated with a certain program may be quite different from children not affiliated with that program. The second aim of this study is to use a new database of all identified DHH children between 0 and 3 years old in California to recruit a large sample that includes children across the full spectrum of interventions and language backgrounds. We will document patterns in family language planning, participation in early intervention, and early language skills in whatever language(s) children are learning. This will provide crucial information about how often children receive various interventions, how often they achieve age-appropriate language skills, and whether there are any disparities in access to early intervention support and language outcomes. The third aim is to validate a new multi-lingual language assessment designed for DHH children. The findings from this study hold the potential to inform evidence-based interventions, enhance early childhood language planning, and pave the way for improved outcomes and opportunities for DHH children by fostering their language development and overall well-being.

NIH Research Projects · FY 2025 · 2024-06

PROJECT SUMMARY/ABSTRACT B cell memory generated by antigen exposure consists of antibodies and memory B cells (MBCs). The human spleen is well recognized as a major MBC reservoir, but recent studies suggest that its role goes beyond MBC storage. There is evidence that MBCs in the spleen receive signals that modify phenotype and function. In addition, it has been proposed that the spleen serves as an archive of all MBC clones that disperse from sites of formation via the blood. Our objective is to perform the first antigen-specific evaluation of the spleen as an evolving MBC archive that represents an individual’s MBC response potential. We will use the influenza A virus hemagglutinin (HA) as a model antigen, since most adults have a large pool of HA-reactive MBCs modified by multiple exposures to variant HA strains and often retaining an imprint of early-life infection. We will test hypotheses about the composition a splenic HA-reactive MBC archive based on our current strong understanding of HA-specific B cell responses and MBC formation in humans. Experiments will be performed using a large collection of stored splenocytes from surgically removed trauma spleens. Under Aim 1, we will test the hypothesis that the size of splenic MBC populations reactive to HA strains and to the conserved HA stalk domain reflect early-life imprinting. The size of MBC populations will be determined by in vitro stimulation of splenic MBCs and measurement of secreted HA-reactive antibodies by multiplex binding assay. Association of HA reactivity with phenotypic MBC subsets will be analyzed by flow cytometry using 29 surface markers and a set of HA probes. Under Aim 2, we will test the hypothesis that an evolving splenic archive mostly contains large numbers of MBCs that are broadly HA cross-reactive. Individual HA+ MBCs will be index sorted and stimulated to induce antibody-secreting cell formation. Clonal antibodies in culture supernatants will be analyzed to determine HA reactivity and affinity. To evaluate the completeness of the splenic archive, Aim 3 studies will test the hypothesis that the archive contains families of clonally-related MBCs with ranges of somatic hypermutation and reactivities to HA strains recognized only in early life, chronological ranges of HAs that frequently include early HAs, and sets of contemporary HAs. Splenocyte samples shown under Aim 2 to contain MBCs with an early-life HA imprinting signature will be selected for multivariate single cell analysis. Immunoglobulin heavy chain variable gene sequencing, calculation of mutation frequencies, and evolutionary tree analysis of clonal clusters will be performed and correlated with HA reactivity profiles. We expect our investigation of the spleen as an archive of HA-reactive MBCs to extend our understanding of the spleen as a key determinant of an individual’s MBC-mediated immunity. This information is essential for a full appreciation of the potential consequences of splenectomy, disease states associated with hyposplenism, B cell depletion therapies, and splenic changes associated with infections.

NIH Research Projects · FY 2026 · 2024-05

PROJECT SUMMARY Cryptosporidiosis, a disease caused by the protozoan parasite Cryptosporidium, poses a significant global health threat, particularly affecting young children in developing regions and immunocompromised individuals. Despite its severity, there are currently no vaccines or effective therapies available, highlighting the urgent need for innovative solutions. This research proposal addresses this critical gap by focusing on two key objectives: establishing reliable small mouse models of cryptosporidiosis and unraveling the intricacies of IFN-γ responses during C. parvum infection. Our preliminary data underscore the significance of the TLR11/TLR12 complex in detecting Cryptosporidium and regulating IFN-γ-mediated immune responses. Additionally, we have developed mouse models with cell-specific deficiencies in IFN-γ production and responsiveness, providing valuable tools to enhance our understanding of host defense against Cryptosporidium. The primary objective of this project is to elucidate the fundamental pathways governing the host's ability to combat C. parvum infections at mucosal sites. To achieve this, our research is structured around specific aims that explore the roles of TLR and IFN-γ pathways in mucosal immunity. This knowledge will provide insights into the molecular and cellular responses that ultimately determine the outcome of C. parvum infections at mucosal sites. Our research endeavors aim to contribute to the development of innovative strategies to combat this devastating disease.

NIH Research Projects · FY 2026 · 2024-05

Microvascular insufficiency and in turn, tissue ischemia and necrosis, contribute to a variety of chronic diseases, and can be an adverse outcome of common reconstructive and plastic surgeries. The goal of this project is to advance a novel ultrasound-based technology to induce neovascularization directly in vivo, and thereby enhance local tissue perfusion. Acoustic patterning utilizes radiation forces associated with an ultrasound field to rapidly and non-invasively organize cells or microparticles volumetrically into defined geometric assemblies. We have shown that in vitro acoustic patterning of endothelial cells within collagen hydrogels leads to the formation of three-dimensional microvascular networks, and that acoustic field parameters employed for patterning influence microvessel morphology. In our recent studies, in vivo acoustic patterning of endothelial cells within injectable hydrogels resulted in formation of perfused microvascular networks in a murine model, providing the first proof- of-concept demonstration that non-invasive, acoustic cell patterning can be used to fabricate functional microvascular networks directly in vivo. An important advantage of ultrasound is its ability to propagate through tissue as an acoustic beam, thus offering avenues to rapidly translate this technology toward in vivo tissue regeneration. Research and development in three key areas are necessary to advance acoustic patterning towards clinical translation: i) development of systematic protocols to fabricate functional microvessel networks within patterned hydrogels, ii) engineering innovative instrumentation for acoustic patterning in vivo, and iii) demonstrated efficacy of the technology in a preclinical model. We address these key areas as follows. Aim 1 will identify sets of acoustic parameters, along with hydrogel and cell combinations, that give rise to functional microvascular networks, in a manner that allows for predictable control over the morphology of three-dimensional microvascular networks. Aim 2 will advance two acoustic instrumentation systems, a dual-transducer system and a phase holographic lens transducer, to provide versatile systems for efficient, site-specific patterning in vivo. Aim 3 will evaluate the efficacy of our in vivo acoustic patterning strategies using mouse models of tissue vascularization and ischemia. Completion of this project will advance in vivo acoustic patterning technologies for tissue vascularization to address a range of clinically relevant scenarios of tissue ischemia.

NIH Research Projects · FY 2026 · 2024-05

PROJECT SUMMARY The goal of this project is to determine how developmental exposure to a mixture of per- and polyfluoroalkyl substances (PFAS) disrupts humoral immune defenses against respiratory virus infection. There is evidence that PFAS affect the immune system, but uncertainty about underlying cellular mechanisms. This project builds on preliminary evidence that developmental exposure to a mixture of PFOA, PFOS, PFNA and PFHxS perturbs the response to influenza A virus (IAV) infection, including significantly fewer T follicular helper (Tfh) cells. Tfh cells are critical drivers of humoral immunity, controlling antibody production, isotype switching, affinity maturation, and immunological memory. Additional pilot data show that fewer Tfh cells in PFAS-exposed offspring correlate with reduced IAV-specific antibody levels. Our results are exciting because, although changes in antibody levels are often associated with PFAS, how developmental PFAS exposure alters key cellular events that underpin humoral immunity is not known. The proposed research will test the central hypothesis that developmental exposure disrupts Tfh cells, which contributes to alterations in B cell responses and antibody production. During IAV infection, we can track responses of Tfh cells, germinal center B cells, and plasma cells over time using multidimensional flow cytometry, and the kinetics of primary and anamnestic responses to IAV are well established. The first aim will define the contribution of alterations in T cells and B cells to the effects of developmental PFAS exposure on Tfh cells and anti-viral humoral immunity, including memory responses. The second aim will delineate key parameters of developmental immunotoxicity of PFAS, including the critical window during development that is most sensitive to PFAS exposure, and the dose-dependent and sex-dependent nature of immune function changes caused by developmental PFAS exposure. This will include using ultra-high- performance liquid chromatography coupled with high-resolution mass spectrometry to measure PFAS in the offspring, allowing internal dose and immune function to be directly related. The third aim will identify the mode of action through which PFAS affect immune function using conditional knockout mice and pharmacological agents. This aim will resolve whether developmental immunotoxicity is mediated via peroxisome proliferator activated receptors (PPAR). This research project will significantly advance knowledge of how developmental exposure to a representative real-world PFAS mixture modulates the immune system. Major impacts include that it will pinpoint cellular targets that contribute to clinical consequences, provide a framework to understand sex differences in PFAS developmental immunotoxicity, produce new information to guide research in human population studies, and refine our ability to identify at risk populations.

NIH Research Projects · FY 2026 · 2024-05

Abstract Meaning in speech is conveyed by time-varying structures, such as phonemes and words, that have highly variable durations. As a consequence, there is a fundamental difference between integrating across physical time (e.g., 100 ms) and speech structure (e.g., a phoneme). Auditory neurophysiology models typically assume that neural integration is yoked to physical time, while many psycholinguistic theories posit that integration in speech is yoked to abstract structures such as phonemes. At present, very little is known about whether neural computations in the cortex are yoked to time or structure. As a consequence, it is unclear if there is a change from time- to structure-yoked integration across the cortex, and if so, where this transition occurs and what types of structures and computations might explain it. Filling this knowledge gap is essential to linking auditory models and cognitive theories, constructing integrated neurocomputational models of auditory-speech processing, and understanding how auditory deficits and neurological disorders impact the neural computations that underlie speech perception. Here, we fill this knowledge gap by systematically testing whether neural integration windows throughout the human cortex are yoked to time or structure and developing unified computational models that can account for both time- and structure-yoked computation in the brain. Our experimental approach is to rescale the duration of all speech structures (e.g., using stretching/compression) and measure the extent to which the neural integration window rescales with structure duration. We measure integration windows using temporally precise intracranial recordings from human neurosurgical patients, combined with a novel experimental method that makes it possible to estimate integration windows from highly nonlinear systems like the brain (Aim I). We also use the dense, whole-brain coverage of functional MRI to spatially map time- and structure-yoked integration (Aim II), and we leverage statistical decomposition techniques developed by the PI to integrate our intracranial and fMRI data. Finally, we use encoding models to directly examine the neural integration of specific, theoretically important acoustic features and speech structures, as well as develop new computational models that can explain time- and structure-yoked integration in a common framework (Aim III). Preliminary data suggest there is a transition from time- to structure-yoked integration across the putative cortical hierarchy with weak structure yoking in the superior temporal gyrus, where selectivity for speech structure first emerges, and strong structure yoking in higher-order regions of the superior temporal sulcus that integrate over longer multi-second timescales. We also show that deep neural networks trained to recognize speech structure directly from sound learn to integrate across speech using short time-yoked windows at early layers and long structure-yoked windows at later layers, providing a promising model to account for our neural data and helping to bridge the gap between traditional auditory and psycholinguistic theories.

NIH Research Projects · FY 2026 · 2024-05

Understanding how the auditory system codes complex sounds benefits from computational models that can predict data collected using different techniques (i.e., psychophysics vs. physiology), different species (i.e., human vs. animal models), and different stimuli (i.e., tones vs. speech). Existing models often focus on modeling individual stages of the system, such as the auditory periphery (e.g., Zilany et al., 2014) or particular binaural circuits (e.g., Wang et al., 2014). However, understanding masking in complex sounds, which is shaped by numerous peripheral and central factors of auditory processing, demands models that integrate multiple aspects of processing, heretofore considered separately, that jointly influence the issues under investigation. Some of these aspects are well established, such as peripheral filtering and transduction, or binaural integration in the subcortex, which gives rise to release from masking due to binaural cues. Others are emerging and have generated active debates in the field, including the effects of efferent control of cochlear gain and the sensitivity of midbrain neurons to modulated inputs, both of which have been linked to masking (or release from masking) in complex sounds. This proposal describes a new computational model of the human auditory subcortex that integrates these aspects of auditory processing and plans to apply it to investigate masking in complex sounds in both normal-hearing and hearing-impaired listeners. The model, which is built upon established descriptions of the mammalian auditory periphery (Zilany et al., 2014; Farhadi et al., 2023), simulates ascending binaural processing up to the level of the inferior colliculus (IC), the binaural hub of the auditory midbrain, as well as descending efferent pathways that regulate cochlear gain. Aim 1 focuses on binaural aspects of the model, and tests whether simulated responses from this model can predict human behavioral performance in binaural-detection tasks, including predictions for individual trials. Aim 2 focuses on the efferent aspects of the model, and tests whether simulated efferent gain control can predict human behavioral performance in tasks that feature a target stimulus preceded by a precursor, which could activate the efferent system and reduce cochlear gain during the target. Aim 3 uses a model with both binaural and efferent pathways and tests whether it can predict intelligibility of speech in complex backgrounds, including spatial separations and binaural phasic manipulations of target and masker. Predictions of data from listeners with and without sensorineural hearing loss will be included for several of the above tasks. The overarching hypothesis is that simulated binaural IC activity can predict performance of both normal-hearing and hearing-impaired listeners across a wide range of behavioral tasks. The proposed research will clarify how peripheral changes associated with hearing loss affect neural coding in central binaural nuclei and interact with control of cochlear gain via the MOC system, enabling the development of better algorithms for restoring normal auditory function via hearing aids and cochlear implants.

NIH Research Projects · FY 2026 · 2024-05

Energy Metabolism in Osteoblasts and Bone Health Energy metabolism is an important regulator of cell fate and tissue homeostasis while its dysregulation is a hallmark of aging in various tissues, including bone. Data on energy metabolism in osteoblasts (OB) are contra- dictory, claiming OB reliance either on aerobic glycolysis or mitochondrial oxidative phosphorylation (OxPhos). With regards to bioenergetic substrates, glutamine and fatty acids were recently shown to be as important for OBs as glucose; and they are metabolized mostly in mitochondria. Our new exciting data suggest an explanation to the above controversies and can reconcile the opposing views on OB metabolism. First, we confirmed that in OBs, glucose metabolites do not reach the mitochondrial Krebs cycle but mostly flow into the pentose phosphate pathway (PPP) and little into pyruvate and lactate. Actively proliferating and synthetic OBs likely benefit from this setup as PPP provides NADPH for redox reactions, nucleotides, etc. Second, we found that OB mitochondria actively metabolize glutamine, supplying not only the Krebs cycle but also cytosolic pyruvate and lactate due to the malate-aspartate shuttle (MAS) activity and ensuing cytosolic reactions. This suggests a regulatory role of mitochondria in the glycolytic process and PPP in OBs. Third, we found that in aged bone, there is mitochondrial dysfunction and increased glucose metabolism to lactate and away from the PPP, and signs of oxidative stress. Systemic inhibition of glucose flux to lactate using lactate dehydrogenase (LDH-A) inhibitor, oxamate, reverses the glycolytic shift and ‘rejuvenates’ bone in aged mice. Our hypothesis is that in OBs, glucose preferential flux into the PPP and glutamine-dependent mitochondrial activity supporting glycolysis and the PPP, is required for bone maintenance and can be restored in aging by targeting LDH-A. This will be tested by characterizing the role of PPP in OBs using loss-of-function (LOF) of G6PD, a key PPP enzyme (Aim 1); confirming the role of mitochondria in supporting glycolysis and the PPP in OBs using inhibition of glutaminolysis or MAS (Aim 2); and confirming LDH-A as a therapeutic target to reverse bone metabolic changes and aging using LDH-A LOF in OBs (Aim 3). Altogether, this is expected to significantly enhance our understanding of how cell energy metab- olism determines OB differentiation and function, explain existing controversies in the field, and suggest new therapies for bone aging.

NIH Research Projects · FY 2026 · 2024-04

We propose to study extracellular vesicles (EVs) as novel mediators of the pathogenesis of radiation cystitis (RC), which affects approximately 15% of prostate cancer (PCa) patients treated with radiotherapy (RT). Bladder radiotoxicity impacts the lives of PCa survivors, most notably older patients, and there are no predictive markers associated with its incidence, nor are there durable molecular therapies capable of preventing RC. There is an urgent need for the development of effective medical countermeasures against RC and the identification of molecular diagnostics to aid in mitigating this debilitating treatment-related complication. EVs are lipid-bound nanoparticles that mediate intercellular communication by delivering cargo molecules to neighboring or distant cells. Studies have shown that RT induces EV release and alters the composition of these EVs. However, most research to date has been conducted in cell lines, with limited preclinical studies and no human research. Using preserved samples collected from a genome-wide association study (GWAS), we reported for the first time a link between urinary EV (uEV) levels and the future onset of hematuria, providing a promising biomarker that may enable more timely treatment of at-risk patients to mitigate the development of late bladder toxicities. The prognostic utility of EVs in serum was less robust. This is further supported by an animal study showing a correlation of uEV particle counts with RT-induced bladder toxicity. Critically, post-RT uEVs derived from PCa patients who developed late hematuria induced substantial oxidative stress in normal bladder recipient cells, further supporting a functional link between EVs and radiotoxicity. Proteomic analyses of 12 uEV samples revealed that those EV cargo proteins were profoundly altered by RT. Notably, we identified 60 RT-toxicity signature uEV proteins including many with functions associated with innate immunity and neutrophil activity, highlighting potential mechanism(s) of action. Based on these studies, we hypothesize that RT induces the release of EVs and alters their composition, and the resultant RT-EVs carry immunologically active biomolecules, thereby inducing additional cellular damage. The kinetics of RT-EV release and RT-EV cargo molecules can serve as predictive biomarkers for RT-induced toxicity that will allow for early intervention to mitigate RT toxicity. We propose three Specific Aims. Aim 1: To define the roles of radiation-induced extracellular vesicles in mediating RT-induced bladder damage in vitro and in vivo. Aim 2: Characterization of RT-EV cargo molecules and their roles in mediating radiotoxicity. Aim 3: To establish body fluid-derived EV-based predictive biomarkers for RT-induced toxicity. Accomplishing the proposed studies will define the functional roles of RT-EVs as mediators of RT toxicity. RT-induced EV release kinetics and alterations in EV cargos will represent sensitive, noninvasive urine/blood-based EV biomarkers that can predict clinically relevant RT outcomes before the onset of late toxicities.

NIH Research Projects · FY 2026 · 2024-04

Project Summary Disruption of the molecular circadian clock is indicative of poor prognosis in non-small cell lung cancers (NSCLCs), but direct evidence for a causal link between circadian clock deregulation and malignancy in human cancer is missing. We found that BMAL1 is downregulated in human NSCLCs, indicative of circadian disruption, low BMAL1 is an indicator of aggressive disease and poor prognosis. In addition, deletion of BMAL1 in a mouse model of NSCLC accelerates cancer progression. These data suggest that BMAL1, and by extension, circadian rhythms, exert a tumor-suppressive role in lung cancer. However, how BMAL1 restrains tumorigenesis and the mechanisms involved in suppression of BMAL1 remain unclear. A potential cause for BMAL1 suppression is the upregulation of MYC-family oncoproteins, which are amplified 50% of NSCLCs. We were the first to show that the molecular clock is disrupted by amplified MYC. In addition, our preliminary data suggest that, even in the presence of glucocorticoids, MYC suppresses BMAL1 expression in both NSCLC and normal lung epithelium, and thus disrupts circadian clock oscillation. To date, MYC amplification is the only identifiable cause of this circadian disruption in NSCLC. While CLOCK-BMAL1, and thus, oscillation of the molecular circadian clock, are necessary to maintain normal lung architecture and identity, we found that MYC activation led to loss of normal lung alveolar epithelial identity and induction of inappropriate proliferation. Notably, glucocorticoids have been shown to slow or halt the growth of some NSCLCs in preclinical and clinical studies, and our preliminary data suggest that glucocorticoids fail to suppress proliferation of lung cells when MYC is overexpressed. Taken together, we hypothesize that BMAL1 suppression and circadian disruption by MYC in NSCLC is critical for loss of alveolar cell identity, the emergence of malignancy, and resistance to glucocorticoids. To test this hypothesis, we propose two Aims. In our first Aim, we will interrogate the degree to which MYC suppression of BMAL1 and disruption of the clock drive loss of lung alveolar cell identity and malignant cell transformation. To test this, we will restore BMAL1 expression in MYC-amplified lung organoids, mouse models. As part of this Aim, we will test the hypothesis that MYC prevents BMAL1 from binding its typical DNA targets. We will also test the association between MYC, BMAL1, and malignancy in human tumor samples. This will for the first time demonstrate that MYC disruption of the clock is critical in driving the earliest stages of NSCLC development. In the second Aim, we will test the degree to which MYC and circadian disruption suppress NSCLC response to glucocorticoids. We will determine, using in vitro and in vivo models of NSCLC from mice and human patients, whether MYC overrides glucocorticoid-mediated growth suppression via suppression of BMAL1. We will also determine the mechanism by which MYC controls the glucocorticoid receptor and molecular clock response to glucocorticoids. Overall, these experiments will demonstrate that BMAL1 is a tumor suppressive protein in NSCLC that is disabled by MYC to drive malignancy.

NIH Research Projects · FY 2026 · 2024-04

PROJECT SUMMARY Erythropoiesis is a finely orchestrated process that involves generating a ~2.5 million red blood cells per second to maintain homeostasis and prevent anemia. During terminal maturation, erythroid precursors upregulate erythroid-specific genes while silencing non-erythroid genes in the setting of a cell that is rapidly dividing and a nucleus that is condensing in preparation for enucleation. Our group has shown that regulation of RNAPII activity is an essential determinant of erythroid cell function. During terminal erythroid maturation, RNA polymerase II (RNAPII) levels decline dramatically, becoming a scarce resource allocated to erythroid genes, such as alpha and beta globin. The mechanism(s) by which RNAPII is removed from genes unnecessary to erythroid differentiation and shunted to produce mRNA essential for red blood cell function is unknown. The Integrator Complex (INT) is a multi-subunit machinery that associates with RNA polymerase II (RNAPII) and functions as a critical transcription regulator. It is a broad negative regulator of promoter-proximally paused RNAPII. Integrator subunit 11 (INTS11) houses the RNA endonuclease domain vital for Integrator to cleave nascent transcripts at all RNAPII loci, which is an important activity for transcriptional repression and the processing of eRNA. Although INT is highly expressed in maturing erythroid cells, little is known about its function in erythropoiesis. Further, the role of promoter-proximal transcriptional termination in regulating erythroid gene expression has been almost completely unexplored. Our preliminary data reveal that disruption of INT impairs the proliferation and maturation of primary human erythroid cells. Our CUT&RUN analyses in primary erythroid cells uncover that INT is present at genes containing stably paused RNAPII that is subsequently lost before enucleation. Finally, we find that INT binds to erythroid enhancers, including the beta-globin LCR, in a manner correlating with increased transcription. Altogether, these data support a hypothesis where INT enforces RNAPII pausing and termination at non-erythroid genes to maintain RNAPII availability while enhancing the transcription of erythroid genes through eRNA processing. To test this hypothesis, we propose two specific aims: Specific Aim1. Determine the function of the Integrator Complex during terminal erythroid maturation. Specific Aim 2. Delineate mechanisms by which Integrator regulates erythroid gene expression.

NIH Research Projects · FY 2026 · 2024-04

Project Summary/ Abstract In order to do a better job identifying complex molecules with novel bioactivity and suitable bioavailability profiles, chemists need a larger supply of promising small molecules, which requires new methods for their efficient synthesis. However, there are many molecules of interest, both natural and non-natural, that are still difficult to prepare with high efficiency and selectivity. Synthetic chemists are constantly searching for versatile new methods for building densely functionalized molecules that contain vicinal chiral centers and quaternary centers. The development of efficient, stereoselective carbon-carbon bond-forming methods will enable chemists to more effectively prepare biologically relevant target molecules, and enable more detailed study of these compounds for applications as chemical therapies. During this project, strategies will be developed to enable efficient, convenient, and stereocontrolled synthesis of highly functionalized cyclic carbocycles and heterocycles from simple precursors, with the formation of two or more carbon-carbon bonds. The new methods are expected to deliver differentially functionalized ring systems with useful synthetic handles for further transformations. The chemistry of various cationic intermediates will be exploited to access a series of bioactive complex molecules, including the natural products tubingensins A and B, and polycyclic intermediates related to Daphniphyllum alkaloid natural products. Modern public health challenges demand a drug pipeline full of promising compounds that represent the entire spectrum of biologically relevant small molecules. This project is expected to make an impact at the very inception of the drug discovery process. Successful development of this versatile new method will enable for the synthesis of small, drug-like molecules with unique shapes, and help chemists expand the catalog of compounds available for biological evaluation. Over the course of the project, novel molecules with drug-like properties will be synthesized, characterized, and submitted for biological evaluation through agreements with different screening programs (NCI (both DTP and MTP), HTS facility at Roswell Cancer Center, BU-CMD (Center for Molecular Discovery). In this way, the two- and three step methods that will be developed during these projects, as well as the intermediates prepared during synthetic efforts toward natural product targets, will become tools for chemists and biologists to use in their efforts to discover effective new medicines.

NIH Research Projects · FY 2026 · 2024-03

Project Summary/Abstract Microglia are immune cells that act as the primary rst-responding sentinels in the brain. In response to brain injury, infection, or disease, microglia rapidly react to attack intruders, remove neuronal debris, and restore home- ostasis. In addition to their immune role, microglia have been shown to be critical to normal brain development and function. Although direct comparisons between morphology and function are hard to make, it is clear that changes in microglial morphology correspond to di erent responses to external stimuli and internal functional states. Reactive microglia undergo a series of stereotyped morphological changes that grossly correspond to their di erent immune functions. Additionally, it has been shown that microglial morphology is altered with neuronal activity, demonstrating that changes in their physiological functions are tied to distinct morphologies, even in the absence of pathology. Analysis of alterations in microglial morphology can inform studies of neurodevelopment, neurodegenerative diseases, and the e ects of environmental toxicants on brain function; however, currently we are unable to ascribed speci c functions to morphological states. Improved methods of processing and analysis have the potential to remove this critical barrier and allow us to directly link morphological changes with their corresponding functional consequences. Confocal microscopy is used to capture digital images at the spatial resolution necessary to detect the morphol- ogy of individual microglia. These images are often processed using proprietary commercial software to extract individual cells. The morphology of these cells is then quantifying using Sholl Analysis, in which concentric circles are overlaid on the image and the number of microglial branches that intersect the circle at each distance from the soma are counted. The resulting curves are subsequently analyzed to obtain summary statistics, such as the maximum number of intersections observed. The majority of these summaries ignore the dependence between adjacent distances and lack a corresponding measure of uncertainty. Furthermore, current methods discard a vast amount of information present in both the Sholl curves and, to an even greater degree, in the digital images themselves. Finally, individual quantitative summaries are typically analyzed separately, ignoring the dependence between di erent aspects of microglial morphology and thereby reducing statistical power. We propose to develop statistical methods to model microglial morphology that fully leverage the wealth of information present in the imaging data and provide interpretable parameter estimates and corresponding measures of uncertainty. The overall goal of the proposed research is to develop statistical methodology that will lead to improved analysis of microglial images and uncover the changes in morphology that are most predictive of alterations in microglial function.

NIH Research Projects · FY 2026 · 2024-03

Human health is inextricably tied to the Great Lakes, which hold 20% of the Earth's surface freshwater. The Lakes experience wide variations in abiotic conditions including water temperature, pH, storm frequency and runoff, ice cover, and precipitation. Human debris, including plastic, also impacts the Lakes and those who rely on them. Plastic enters the Lakes as microplastic (MP; particles <5 mm) or as macro debris that may degrade to MP. There are significant knowledge gaps about the cycle of plastic in the Lakes, but MPs have been found in all lake habitats, throughout the food chain, and in tap water. The potential human health effects of Lake associated exposure to MP are vastly understudied. How MP inputs, fate and impacts are affected by spatial and temporal heterogeneity present in the watershed and nearshore regions of the Lake is also unknown. Addressing such complex problems requires engaging multiple community partners and a multidisciplinary systems science approach. The over-arching goal of the Lake Ontario Center for Microplastics and Human Health is to prevent negative human health impacts of MP in the Great Lakes by engaging multiple partners in research, supporting environmental health literacy, and informing solutions. Because the Lake Ontario region is representative of the Great Lakes basin, our work will be broadly transferable. Our innovative approach assesses plastics as they exist in the environment: as mixtures of post-consumer plastic polymers, degraded by the environment, and covered with biofilm. A major challenge of MP research is standardization of materials and methods, which we address with a novel Materials and Metrology Core that supports and is integral to all 3 research projects. Project 1 will holistically assess plastic input, degradation, ecotoxicity, and microorganisms in plastic-associated biofilms. Project 1 culminates in modeling input, fate and transport of microplastics in Lake Ontario. Project 2 will build on Project 1's foundation to assess the potential for dermal and lung exposure to MPs by leveraging nanomembrane technologies to analyze mammalian cytotoxicity and bioactivity of natural and experimental particle mixtures in combination with variation in temperature and availability of metals and persistent organic pollutants. Project 3 extends the investigation to the whole organism by using the amphibian Xenopus to rigorously assess the biodistribution of MPs and impacts on development, fitness, immune homeostasis and antiviral immunity, under varied conditions of temperature. Given the high degree of evolutionary conservation of vertebrate physiology, the outcomes from this study are very relevant to human health. Our Community Engagement Core involves multiple partners in all aspects of the Center, including community science, direct action, development and dissemination of materials, and building partners' capacity. Our Administrative Core coordinates across two institutions (the University of Rochester and the Rochester Institute of Technology), supports multidirectional communication with external stakeholders, and evaluates progress toward Center goals.

NIH Research Projects · FY 2026 · 2024-03

Abstract Chemosensation plays a critical role in social behavior among humans and mammals. Olfaction, a form of chemosensation, is essential for various social behaviors, including maternal behavior and predator detection. For terrestrial mammals, social interaction is heavily reliant on chemosensory information processed by the accessory olfactory system (AOS), which is specialized for detecting non-volatile odorants, such as kairomones (interspecific social cues) and pheromones (conspecific social cues). In the AOS, the initial processing of chemosensory information takes place in the vomeronasal organ (VNO), where natural AOS ligands activate vomeronasal sensory neurons (VSNs) through the expression of vomeronasal receptors (VRs). Despite extensive research, many unknowns exist regarding the natural AOS ligand-receptor pairs, elicited behavior, and the downstream neural circuitries. My preliminary data revealed that various types of molecules, such as bile acids, dipeptides, and fatty acids, had distinct levels of abundance in the feces of mouse-fed snakes compared with those from insect-fed lizards and salad-fed turtles. In addition, the AOS was selectively activated by fecal extracts from reptiles fed different diets. To explore how mice respond to snake fecal chemosignals, I developed a layered, hybrid machine learning (ML)-based behavior analysis workflow. This workflow revealed that snake feces increased risk assessment behaviors in mice that were distinct from other threatening odors, such as 2,4,5-Trimethylthiazole (TMT). Based on these preliminary data and analytic tools, this proposal seeks to identify the chemosensory mechanism and associated behaviors elicited by threatening chemosignals from the snake, a known mouse predator. To do this, I will use liquid chromatography-mass spectrometry (LC-MS) to determine the natural fecal ligands that activate VSNs. Then, I will implement volumetric VNO Ca2+ imaging via objective-coupled planar illumination (OCPI) microscopy to identify responsive VSN populations to natural fecal ligands. I will also leverage novel ML-based analytic workflow to comprehensively quantify mouse behavior from 2D/3D video monitoring as animals respond to fecal chemosignals from predatory species. Furthermore, I will employ whole-brain serial two-photon tomography (STPT) imaging to determine brain-wide activity patterns elicited by threatening predatory chemosignals. Collectively, this proposal will significantly advance the field by (1) identifying new kairomone ligands, (2) broadening the range of analytical techniques for studying chemosensory behavior, and (3) deepening our understanding of chemosensory information processing along the behaviorally relevant AOS pathway. The successful completion of the proposed experiments will provide a strong foundation for a R01 grant, including uncovering AOS ligand-receptor interactions at the single-cell level (Aim 1), examining associated behaviors in high resolution (Aim 2), and exploring the activity patterns triggered on a brain-wide scale (Aim 3).

NIH Research Projects · FY 2026 · 2024-03

Project Summary/Abstract Chemosensory systems contribute extensively to social behavior in humans and other mammals, including mice, a predominant animal model for diseases and disorders that impact human social function. We propose to study the neural circuitry of the accessory olfactory system in order to better understand how this system extracts information from chemical messages and informs social behavior. Without improved understanding of these processes, we risk making mistakes in the interpretation of studies seeking new therapies for diseases and disorders involving social behavior. The activity of excitatory projection neurons called mitral cells (MCs) in the first neural circuit in the accessory olfactory system, called the accessory olfactory bulb (AOB), strongly influences reproductive physiology and social behavior. AOB mitral cell activity is tightly controlled by several types of GABAergic interneurons: juxtaglomerular cells, external granule cells, and internal granule cells (IGCs). We and others have identified that AOB IGCs undergo experience-dependent plasticity following chemosensory social behaviors. We will investigate the hypothesis that these cells, and perhaps other AOB interneurons, are involved in social behavior plasticity. We will use multiple physiological techniques to investigate cellular and synaptic physiology in AOB interneurons that undergo experience-dependent plasticity. We will investigate how experience- dependent plasticity modulates interneuron excitability, morphology, and gene transcription. We will determine how interneuron plasticity influences MC chemosensory tuning in vivo and ex vivo using chemogenetics, optogenetics, and live calcium imaging. Finally, we will investigate the impacts of inhibitory plasticity on brain-wide patterns of neuronal activation and social behavior during repeated social encounters. Combined, these studies will fill major gaps in our understanding of chemosensory information processing, experience-dependent plasticity, and mammalian social behavior.

NIH Research Projects · FY 2026 · 2024-02

Upon infection, numerous cell types secrete anti-viral cytokines that induce an anti-viral state in neighboring cells, which is critical for limiting infection. This proposal focuses on two opposing aspects of this anti-viral state: one, cytokine-induced metabolic reprogramming, which we find is essential for the ability of cytokines to limit viral infection; and two, the Human Cytomegalovirus (HCMV) UL26 protein, which we find is a major antagonist of anti-viral gene expression. HCMV is a major cause of congenital birth defects and causes severe disease in several immunosuppressed patient populations. Our results indicate that the anti-viral cytokine TNFα induces glycolytic activation, which is essential for its anti-HCMV activity. However, the mechanisms involved are not clear. We propose to identify the mechanisms through which anti-viral cytokines induce metabolic remodeling (Aim 1), and determine how cytokine-induced metabolic activities limit HCMV infection (Aim 2). Finally, we will determine how the HCMV UL26 protein blocks anti-viral responses, which we hypothesize involves modulation of the activity of an intrinsic immune transcription factor complex (Aim 3). The proposed research will identify novel cellular and viral mechanisms that govern the success of HCMV infection. These mechanisms represent key determinants that could potentially be targeted to limit virally-associated pathogenesis.

NIH Research Projects · FY 2025 · 2024-02

Abstract: Transcription is one of the first steps in gene expression, and the many protein factors involved must be tightly regulated to correctly carry out cellular processes. The Integrator complex, a 15-subunit metazoan- specific complex, was initially discovered to be crucial for the proper transcription of certain non-coding RNAs. Recently, it has been found that Integrator is a broad transcriptional regulator with roles at many protein-coding and non-coding genes. Integrator acts as a negative regulator of RNA Polymerase II (RNAPII) transcription through promoter-proximal termination and can alter its functionality in response to stress, such as DNA damage or reactive oxygen species. Despite its critical role in fine-tuning transcriptional regulation, it is not yet understood how Integrator is assembled and regulated, presenting a knowledge gap in the field. Our preliminary experiments strikingly revealed that a key factor involved in DNA damage repair (DDR) associates with a global regulator of RNAPII activity, thus providing a previously unknown connection between these two processes. Specifically, the BRCA1-ATM activator 1 (BRAT1) associates with Integrator subunit 11 (INTS11), the endonuclease-containing subunit within the Integrator complex. BRAT1 is a cytoplasmic protein that re-localizes to the nucleus upon DNA damage to act as a scaffold between the site of damage and repair proteins. Our cryo-EM analysis of the INTS11-BRAT1 heterodimer reveals that BRAT1 forms a circular structure around INTS11 and uses three conserved C-terminal residues to bind to the INTS11 active site, preventing its cleavage of RNA. Additionally, the cryo-EM analysis showed that INTS9 can bind to form an INTS11-INTS9- BRAT1 heterotrimer, suggesting interplay between BRAT1 as an inhibitor of INTS11 and other members of the Integrator complex. The goal of this proposal is to examine the function and mechanism of action of these two unique complexes. To examine the function, our lab generated BRAT1 null cell lines and a rapid depletion system using the auxin-inducible degron (AID) tag to allow quick depletion of INTS11. Initial studies of these lines show that BRAT1 loss results in an INTS11 depletion phenotype, presenting upregulation of genes negatively regulated by Integrator. Overall, these data present a model where BRAT1 could regulate Integrator activity through its association with INTS9/11. The hypothesis is that BRAT1 acts as a licensing factor, facilitating the assembly of the Integrator complex and providing precise regulation, which is especially important during cellular stress such as DNA damage. To test this hypothesis, three aims are proposed. First, the interaction between BRAT1 and INTS9/11 will be biochemically defined to further probe the structure. Next, the impact of BRAT1 on the canonical Integrator complex function will be determined. Finally, the impact of INTS11-INTS9-BRAT1 during DNA damage repair will be elucidated. Successful completion of these aims will provide a more thorough understanding of the regulation and assembly of the Integrator complex.

NIH Research Projects · FY 2026 · 2024-01

Abstract (Overall) The University of Rochester (UR) and Duke University will establish a Translational Center for Barrier MPS (TRaCe-bMPS) to create drug development tools (DDTs) focused on the role of barrier functions in disease, injury, and infection. The overall goal of the Center is to submit full qualification packages to the FDA for five DDTs relevant to the treatment of: 1) central nervous system (CNS) disorders, 2) fibrosis, 3) musculoskeletal autoimmune disease, 4) sepsis, and 5) osteomyelitis. For each DDT we have assembled an experienced and multidisciplinary team to establish reproducibility of biomarker assessments for clinically important contexts of use (CoU). Each DDT will be based on an existing, validated MPS model and leverage the modular µSiM MPS platform which provides design flexibility along with translationally relevant permeability and imaging at the interface between tissue compartments. The TRaCe-bMPS will comprise: 1) a Qualification Program (QP), 2) a Resource Core (RC), and 3) an Administrative Core (AC). These units will work together to achieve the Center’s five-year mission while establishing sustainability through commercialization, collaboration, and resource sharing. The QP will develop DDTs and standard operating procedures (SOPs) and achieve answer-in-sample-out functionality through live cell imaging and integrated sensor technologies. Reproducibility for each DDT will be established in at least two laboratories. Qualification plans and packages will be submitted to the FDA in a collaboration between regulatory scientists at UR and Duke. Working with manufacturers, the RC will qualify every DDT component before distribution to development teams. The RC will also advance DDTs to arrayed formats that are compatible with automated plate readers and liquid handlers. The AC will include an Executive Committee that will direct the Center with input from stakeholders, including pharmaceutical companies who will define end user needs. The AC will also manage formal reporting and other interactions with the NIH, FDA, and the NCATS center hub. The dysregulated transport of cells and molecules between tissues is the underlying cause of many diseases and is applicable to the development of drug programs. Additionally, the delivery of drugs to affected tissues depends on the ability to cross these barriers. Despite the fundamental significance of tissue barriers in medicine, most microphysiological systems (MPS) do not provide reliable access to quantitative assessments cellular and molecular exchanges at tissue barriers. By focusing on DDTs specially designed to provide these metrics, the TRaCe-bMPS addresses an unmet need in drug development. This focus, along with the unique technologies that enable it, will also make the TRaCe-bMPS a unique and valuable contributor to the forthcoming TRaCe-MPS network.